Microbes contribute to aquatic ecosystem function and the fitness of macroscopic organisms, including zooplankton. Many factors affect the taxonomic compositions of free-living (bacterioplankton) and zooplankton-associated microbial communities in lakes, yet how these communities vary seasonally and among lakes remains poorly understood. Here we investigate how free-living bacterial communities and those associated with different crustacean zooplankton hosts change in response to fluctuations in their natural environment across time and space. Here we use repeated sampling of bacterioplankton, zooplankton communities, zooplankton microbiomes (16S-rRNA), and water chemistry parameters of six lakes in the eastern Sierra Nevada mountains of California across a summer season. We tested the influence of environmental conditions and spatial proximity as drivers of free-living and host-associated zooplankton. In addition, we tested whether microbiomes of zooplankton were distinct or similar among taxonomically diverse hosts and whether space or host identify best structured these communities.
knitr::opts_chunk$set(warning=FALSE, message=FALSE, fig.align='center', cache=TRUE)
# load packages
if (!require("pacman")) install.packages("pacman") # for rapid install if not in library
devtools::install_github("benjjneb/dada2", ref="v1.20") # update to most recent dada2
remotes::install_github("microbiome/microbiome")
remotes::install_github("kstagaman/phyloseqCompanion")
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
if (!require("phyloseq", quietly = TRUE))
BiocManager::install("phyloseq", quietly = TRUE)
if (!require("dada2", quietly = TRUE))
BiocManager::install("dada2", quietly = TRUE)
# use pacman to load CRAN packages missing
pacman::p_load('knitr', 'microbiome', 'phyloseq', 'tidyr', 'tidyverse', 'knitr', 'magrittr', 'effects', 'devtools', 'stringi', 'dplyr', "ggplot2", "gridExtra", "dada2", "phyloseq", "vegan", "cowplot", 'doBy', 'ecodist', 'phyloseqCompanion', 'pairwiseAdonis', 'glue', 'geosphere', 'data.table', 'patchwork', 'car', 'ggcorrplot', 'FactoMineR', 'devtools', 'emmeans', 'rmarkdown', 'reshape', 'lattice', 'plyr', 'magrittr', 'factoextra', 'multcompView', 'decontam', 'factoextra', 'car', 'mia', 'ade4', 'fossil', 'picante', 'reshape', 'readr', 'corrr', 'Hmisc', "MASS", "FSA", "sciplot", "decontam","BiocManager", 'ggpubr', 'ggmap', "ggordiplots", "fossil", "igraph", "huge", "leaflet", "ggtree", "colorBlindness", "RColorBrewer","MicrobiotaProcess", "predict3d", "ggiraphExtra", "data.table", "betapart", "naniar", "rstatix")
The map of lakes and their proximity can be seen below. We sampled zooplankton, water, and biogeochemical variables in lakes in the Eastern Sierra Nevada mountains of California, USA: Eastern Brook, Serene, Convict, Cooney, Blue, and Virginia.